1ZZN

Crystal structure of a group I intron/two exon complex that includes all catalytic metal ion ligands.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural evidence for a two-metal-ion mechanism of group I intron splicing.

Stahley, M.R.Strobel, S.A.

(2005) Science 309: 1587-1590

  • DOI: 10.1126/science.1114994
  • Primary Citation of Related Structures:  
    1ZZN

  • PubMed Abstract: 
  • We report the 3.4 angstrom crystal structure of a catalytically active group I intron splicing intermediate containing the complete intron, both exons, the scissile phosphate, and all of the functional groups implicated in catalytic metal ion coordin ...

    We report the 3.4 angstrom crystal structure of a catalytically active group I intron splicing intermediate containing the complete intron, both exons, the scissile phosphate, and all of the functional groups implicated in catalytic metal ion coordination, including the 2'-OH of the terminal guanosine. This structure suggests that, like protein phosphoryltransferases, an RNA phosphoryltransferase can use a two-metal-ion mechanism. Two Mg2+ ions are positioned 3.9 angstroms apart and are directly coordinated by all six of the biochemically predicted ligands. The evolutionary convergence of RNA and protein active sites on the same inorganic architecture highlights the intrinsic chemical capacity of the two-metal-ion catalytic mechanism for phosphoryl transfer.


    Related Citations: 
    • Crystal Structure of a Self-Splicing Group I Intron with Both Exons
      Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., Strobel, S.A.
      (2004) Nature 430: 45
    • Crystal Structure of a group I intron splicing intermediate
      Adams, P.L., Stahley, M.R., Gill, M.L., Kosek, A.B., Wang, J., Strobel, S.A.
      (2004) RNA 10: 1867
    • In vitro splicing of the ribosomal RNA precursor of tetrahymena: involvement of a guanosine nucleotide in the excision of intervening sequence
      Cech, T.R., Zaug, A.J., Grabowaski, P.J.
      (1981) Cell 27: 487
    • Self-splicing intron in tRNA genes of widely divergent bacteria
      Reinhold-Hurek, B., Shub, D.A.
      (1992) Nature 357: 173

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAINA98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
NIH Common Fund Data Resources
PHAROS  P09012
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
197-MERB197N/A
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP*GP*CP*C)-3'C22N/A
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5'-R(*CP*AP*(5MU))-3'D3N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    K
    Query on K

    Download CCD File 
    B
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    B, C
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.37 Å
    • R-Value Free: 0.307 
    • R-Value Work: 0.269 
    • R-Value Observed: 0.269 
    • Space Group: P 41 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 108.466α = 90
    b = 108.466β = 90
    c = 246.4γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2005-08-30
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2017-10-11
      Changes: Advisory, Refinement description